Why does exporting FBX to Unity mess up my UVs
I'm having this exact issue, only iv'e used Maya. I created my high poly sculpt in zbrush, then rigged, animated, and UV mapped him in Maya. But the exported fbx has broken UVs in Unity... its maddening.

solution for you there are two UV layers in all imported assets in Unity. In the material inspector, try switching from UV0 to UV1 (in drop-down menu). Hopefully this fixes your problem... If not then you and i are truly in the same boat. Which tells me its likely a Unity problem, since we're using different modeling/animation software.